[cig-commits] commit: Remove json_input directory

Mercurial hg at geodynamics.org
Fri Nov 25 14:52:41 PST 2011


changeset:   435:8630c321b820
tag:         tip
user:        Walter Landry <wlandry at caltech.edu>
date:        Fri Nov 25 11:01:26 2011 -0800
files:       json_input/benchmarks/circular_inclusion.json json_input/benchmarks/divergence.json json_input/benchmarks/divergence3D.json json_input/benchmarks/drucker_prager.json json_input/benchmarks/geomod2004_extension.json json_input/benchmarks/sinusoid.json json_input/benchmarks/sphere_in_cylinder.json json_input/benchmarks/thermal_diffusion.json json_input/benchmarks/thermal_eulerian.json json_input/benchmarks/thermal_lagrangian.json json_input/cookbook/deforming_bottom.json json_input/cookbook/extension.json json_input/cookbook/extension3D.json json_input/cookbook/file.json json_input/cookbook/fixed_bottom.json json_input/cookbook/inflow_outflow.json json_input/cookbook/multi_material.json json_input/cookbook/non_newtonian.json json_input/cookbook/normal_stress.json json_input/cookbook/sinusoid.json json_input/cookbook/split.json json_input/cookbook/template.json json_input/cookbook/thermal.json json_input/cookbook/thermal_file.json json_input/cookbook/thermal_only.json json_input/cookbook/tracers.json json_input/cookbook/viscous.json json_input/cookbook/yielding.json
description:
Remove json_input directory


diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/circular_inclusion.json
--- a/json_input/benchmarks/circular_inclusion.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-{
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "inclusionShape":
-        {
-            "Type": "EquationShape",
-            "equation": "1-(x*x+y*y)"
-        },
-        "backgroundShape":
-        {
-            "Type": "Intersection",
-            "shapes":[
-                "boxShape",
-                "!inclusionShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "inclusionViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "2.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "backgroundShape",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "inclusion":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "inclusionShape",
-            "Rheology": [
-                "inclusionViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-x"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "y"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-x"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "y"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "0",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "80",
-    "maxY": "80",
-    "maxZ": "80",
-    "nx": "64",
-    "ny": "64",
-    "nz": "16",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1"
- }
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/divergence.json
--- a/json_input/benchmarks/divergence.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,162 +0,0 @@
-{
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "topLeftShape":
-        {
-            "Type": "Box",
-            "startX": "-0.01",
-            "endX": "0.01",
-            "startY": "1.99",
-            "endY": "2.01",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "topRightShape":
-        {
-            "Type": "Box",
-            "startX": "1.99",
-            "endX": "2.01",
-            "startY": "1.99",
-            "endY": "2.01",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "bottomLeftShape":
-        {
-            "Type": "Box",
-            "startX": "-0.01",
-            "endX": "0.01",
-            "startY": "-0.01",
-            "endY": "0.01",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "bottomRightShape":
-        {
-            "Type": "Box",
-            "startX": "1.99",
-            "endX": "2.01",
-            "startY": "-0.01",
-            "endY": "0.01",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "divergence":
-        {
-            "Type": "DivergenceForce",
-            "ForceVector": "cont_force",
-            "DomainShape": "boxShape",
-            "force_value": "-2"
-        }
-
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "MeshShapeVC",
-                "Shape": "topLeftShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "topRightShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "bottomLeftShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "-1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "bottomRightShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "-1.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "0",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "2",
-    "maxZ": "2",
-    "nx": "4",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/divergence3D.json
--- a/json_input/benchmarks/divergence3D.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,290 +0,0 @@
-{
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "topLeftFrontShape":
-        {
-            "Type": "Box",
-            "startX": "-0.01",
-            "endX": "0.01",
-            "startY": "1.99",
-            "endY": "2.01",
-            "startZ": "-0.01",
-            "endZ": "0.01"
-        },
-        "topRightFrontShape":
-        {
-            "Type": "Box",
-            "startX": "1.99",
-            "endX": "2.01",
-            "startY": "1.99",
-            "endY": "2.01",
-            "startZ": "-0.01",
-            "endZ": "0.01"
-        },
-        "bottomLeftFrontShape":
-        {
-            "Type": "Box",
-            "startX": "-0.01",
-            "endX": "0.01",
-            "startY": "-0.01",
-            "endY": "0.01",
-            "startZ": "-0.01",
-            "endZ": "0.01"
-        },
-        "bottomRightFrontShape":
-        {
-            "Type": "Box",
-            "startX": "1.99",
-            "endX": "2.01",
-            "startY": "-0.01",
-            "endY": "0.01",
-            "startZ": "-0.01",
-            "endZ": "0.01"
-        },
-        "topLeftBackShape":
-        {
-            "Type": "Box",
-            "startX": "-0.01",
-            "endX": "0.01",
-            "startY": "1.99",
-            "endY": "2.01",
-            "startZ": "1.99",
-            "endZ": "2.01"
-        },
-        "topRightBackShape":
-        {
-            "Type": "Box",
-            "startX": "1.99",
-            "endX": "2.01",
-            "startY": "1.99",
-            "endY": "2.01",
-            "startZ": "1.99",
-            "endZ": "2.01"
-        },
-        "bottomLeftBackShape":
-        {
-            "Type": "Box",
-            "startX": "-0.01",
-            "endX": "0.01",
-            "startY": "-0.01",
-            "endY": "0.01",
-            "startZ": "1.99",
-            "endZ": "2.01"
-        },
-        "bottomRightBackShape":
-        {
-            "Type": "Box",
-            "startX": "1.99",
-            "endX": "2.01",
-            "startY": "-0.01",
-            "endY": "0.01",
-            "startZ": "1.99",
-            "endZ": "2.01"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "divergence":
-        {
-            "Type": "DivergenceForce",
-            "ForceVector": "cont_force",
-            "DomainShape": "boxShape",
-            "force_value": "-3"
-        }
-
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "MeshShapeVC",
-                "Shape": "topLeftFrontShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "-1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "topRightFrontShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "-1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "bottomLeftFrontShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "-1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "bottomRightFrontShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "-1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "topLeftBackShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "topRightBackShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "bottomLeftBackShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "MeshShapeVC",
-                "Shape": "bottomRightBackShape",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "-1.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "0",
-    "outputPath": "./output",
-    "dim": "3",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "2",
-    "maxZ": "2",
-    "nx": "4",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/drucker_prager.json
--- a/json_input/benchmarks/drucker_prager.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,174 +0,0 @@
-{
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "inclusionShape":
-        {
-            "Type": "EquationShape",
-            "equation": "(.01)^2-(x*x+y*y)"
-        },
-        "backgroundShape":
-        {
-            "Type": "Intersection",
-            "shapes":[
-                "boxShape",
-                "!inclusionShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "inclusionViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "0.0001"
-        },
-        "strainWeakening":
-        {
-            "Type": "StrainWeakening",
-            "TimeIntegrator": "timeIntegrator",
-            "MaterialPointsSwarm": "materialSwarm",
-            "softeningStrain": "0.1",
-            "initialDamageFraction": "0.0",
-            "initialDamageWavenumber": "0.5",
-            "initialDamageFactor": "0.5",
-            "healingRate": "0.0"
-        },
-        "yielding":
-        {
-            "Type": "DruckerPrager",
-            "PressureField": "PressureField",
-            "VelocityGradientsField": "VelocityGradientsField",
-            "MaterialPointsSwarm": "materialSwarm",
-            "Context": "context",
-            "StrainWeakening": "strainWeakening",
-            "StrainRateField": "StrainRateField",
-            "cohesion": "cohesion",
-            "cohesionAfterSoftening": "cohesionAfterSoftening",
-            "frictionCoefficient": "frictionCoefficient",
-            "frictionCoefficientAfterSoftening": "frictionCoefficient",
-            "minimumViscosity": "minimumViscosity",
-            "maxStrainRate": "maxStrainRate"
-        },
-        "brittle":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "backgroundShape",
-            "Rheology": [
-                "backgroundViscosity",
-                "yielding",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "inclusion":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "inclusionShape",
-            "Rheology": [
-                "inclusionViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-x"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "y"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "-x"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "y"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "0",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "1",
-    "maxY": "1",
-    "maxZ": "1",
-    "nx": "64",
-    "ny": "64",
-    "nz": "16",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "nonLinearTolerance": "1.0e-3",
-    "linearTolerance": "1,0e-7",
-    "nonLinearMinIterations": "100",
-    "cohesion": "1e-6",
-    "cohesionAfterSoftening": "1e-10",
-    "frictionCoefficient": "1.0",
-    // "minimumViscosity": "1e-4",
-    "maxStrainRate": "100",
-    "journal.info": "True",
-    "journal.debug": "True",
-    "journal-level.info": "1",
-    "journal-level.debug": "1"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/geomod2004_extension.json
--- a/json_input/benchmarks/geomod2004_extension.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,204 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "9.81"
-        },
-        "backgroundShape":
-        {
-            "Type": "EquationShape",
-            "equation": "1"
-        },
-        "pdmsShape":
-        {
-            "Type": "Box",
-            "startX": "0.05",
-            "endX": "0.15",
-            "startY": "0",
-            "endY": "0.005",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "crustShape":
-        {
-            "Type": "Intersection",
-            "shapes":
-            [
-                "backgroundShape",
-                "!pdmsShape"
-            ]
-        },
-        "crustViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0e2"
-            // "eta0": "1.0e12"
-        },
-        "strainWeakening":
-        {
-            "Type": "StrainWeakening",
-            "TimeIntegrator": "timeIntegrator",
-            "MaterialPointsSwarm": "materialSwarm",
-            "initialSofteningStrain": "0.5",
-            "finalSofteningStrain": "1.0",
-            "initialDamageFraction": "0.0",
-            "initialDamageWavenumber": "0.5",
-            "initialDamageFactor": "0.5",
-            "healingRate": "0.0"
-        },
-        "yielding":
-        {
-            "Type": "DruckerPrager",
-            "PressureField": "PressureField",
-            "VelocityGradientsField": "VelocityGradientsField",
-            "MaterialPointsSwarm": "materialSwarm",
-            "Context": "context",
-            "StrainWeakening": "strainWeakening",
-            "StrainRateField": "StrainRateField",
-            "cohesion": "10.0",
-            "cohesionAfterSoftening": "0.1",
-            "frictionCoefficient": "0.726542528005",
-            "frictionCoefficientAfterSoftening": "0.600860619027",
-            "minimumViscosity": "minimumViscosity",
-            "maxStrainRate": "maxStrainRate"
-        },
-        "pdmsViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "5e-6"
-            // "eta0": "50000"
-        },
-        "crust":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "crustShape",
-            "density": "1560.0",
-            "Rheology": [
-                "crustViscosity",
-                "yielding",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "pdms":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "pdmsShape",
-            "density": "965.0",
-            "Rheology": [
-                "pdmsViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "front",
-                "variables": [
-                    {
-                        "name": "vz",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "back",
-                "variables": [
-                    {
-                        "name": "vz",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "6.94444444444e4"
-                        // "value": "6.94444444444e-6"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "(step(x-0.101) + (x-0.099)/(.002)*step(x-.099)*step(0.101-x))*6.94444444444e4"
-                        // "value": "step(1-x)*6.94444444444e-6"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "5000",
-    "outputPath": "./output.extension",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "0.2",
-    "maxY": "0.035",
-    "maxZ": "1",
-    "nx": "64",
-    "ny": "16",
-    "nz": "8",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "linearTolerance": "1e-7",
-    "nonLinearTolerance": "1e-3",
-    "maxUzawaIterations": "5000",
-    "minimumViscosity": "1e-6",
-    "maxStrainRate": "1e6",
-    "journal.info": "True",
-    "journal.debug": "True",
-    "journal-level.info": "1",
-    "journal-level.debug": "1"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/sinusoid.json
--- a/json_input/benchmarks/sinusoid.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "backgroundShape":
-        {
-            "Type": "EquationShape",
-            "equation": "1"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "backgroundShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "surfaceAdaptor":
-        {
-            "Type": "SurfaceAdaptor",
-            "mesh":"v-mesh",
-            "sourceGenerator": "v-mesh-generator",
-            "topEquation": "0.01*cos(2*pi*x)"
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0.0",
-    "minY": "0.0",
-    "minZ": "0.0",
-    "maxX": "0.5",
-    "maxY": "1.0",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "32",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/sphere_in_cylinder.json
--- a/json_input/benchmarks/sphere_in_cylinder.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,184 +0,0 @@
-{
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "cylinderShape": 
-        {
-            "Type": "EquationShape",
-            "equation": "4-hypot(x,z)"
-        },
-        "sphereShape": 
-        {
-            "Type": "EquationShape",
-            "equation": "1-(x*x + (y-4)*(y-4) + z*z)"
-        },
-        "backgroundShape":
-        {
-            "Type": "Intersection",
-            "shapes":[
-                "cylinderShape",
-                "!sphereShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "backgroundShape",
-            "density": "0.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "nonbackgroundShape":
-        {
-            "Type": "Intersection",
-            "shapes":[
-                "!backgroundShape"
-            ]
-        },
-        "highViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "100.0"
-        },
-        "sphere":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "nonbackgroundShape",
-            "density": "1.0",
-            "Rheology": [
-                "highViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "front",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "back",
-                "variables": [
-                    {
-                        "name": "vz",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vz",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "0",
-    "outputPath": "./output",
-    "dim": "3",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "4",
-    "maxY": "8",
-    "maxZ": "4",
-    "nx": "8",
-    "ny": "16",
-    "nz": "8",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/thermal_diffusion.json
--- a/json_input/benchmarks/thermal_diffusion.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
-{
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "alpha": "1.0",
-            "diffusivity": "3.14159",
-            "heatingElements": [
-                {
-                    "Q": "0.0",
-                    "lambda": "1.0"
-                }
-            ],
-            "Rheology": [
-                "backgroundViscosity"
-            ]
-        }
-    },
-    "velocityICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureBCs": {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "temperature",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "TemperatureField"
-    ],
-    "enable-stokes": false,
-    "enable-thermal": true,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "1",
-    "maxY": "1",
-    "maxZ": "0.3",
-    "nx": "8",
-    "ny": "8",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/thermal_eulerian.json
--- a/json_input/benchmarks/thermal_eulerian.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,156 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "T-mesh": "T-mesh",
-                "displacementField": "DisplacementField",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "staticLeft": "True",
-                "staticRight": "True",
-                "staticTop": "True",
-                "staticBottom": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "alpha": "1.0",
-            "diffusivity": "0.0",
-            "heatingElements": [
-                {
-                    "Q": "0.0",
-                    "lambda": "1.0"
-                }
-            ],
-            "Rheology": [
-                "backgroundViscosity"
-            ]
-        }
-    },
-    "velocityICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureBCs": {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "temperature",
-                        "value": "(x<.375 || x>.625 || y<.375 || y>.625) ? 1 : 2"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "TemperatureField",
-        "VelocityField"
-    ],
-    "enable-stokes": false,
-    "enable-thermal": true,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "2",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "16",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/benchmarks/thermal_lagrangian.json
--- a/json_input/benchmarks/thermal_lagrangian.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,152 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "T-mesh": "T-mesh",
-                "displacementField": "DisplacementField",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField"
-            }
-        ]
-    },
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "alpha": "1.0",
-            "diffusivity": "0.0",
-            "heatingElements": [
-                {
-                    "Q": "0.0",
-                    "lambda": "1.0"
-                }
-            ],
-            "Rheology": [
-                "backgroundViscosity"
-            ]
-        }
-    },
-    "velocityICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "vx",
-                        "value": ".3*x-0.2"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "(x+.3)*(1.5-x)*y + (x-.15)*(0.7-x)"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureBCs": {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "temperature",
-                        "value": "(x<.375 || x>.625 || y<.375 || y>.625) ? 1 : 2"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "TemperatureField",
-        "VelocityField"
-    ],
-    "enable-stokes": false,
-    "enable-thermal": true,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "1",
-    "maxY": "1",
-    "maxZ": "0.3",
-    "nx": "8",
-    "ny": "8",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/deforming_bottom.json
--- a/json_input/cookbook/deforming_bottom.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True",
-                "wrapBottom": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-        ,"stressBC":
-        {
-            "Type": "StressBC",
-            "ForceVector": "mom_force",
-            "wall": "bottom",
-            "normal_value": "0.35-y"
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/extension.json
--- a/json_input/cookbook/extension.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/extension3D.json
--- a/json_input/cookbook/extension3D.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,139 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "backgroundShape":
-        {
-            "Type": "EquationShape",
-            "equation": "1"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "backgroundShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "surfaceAdaptor":
-        {
-            "Type": "SurfaceAdaptor",
-            "mesh":"v-mesh",
-            "sourceGenerator": "v-mesh-generator",
-            "topSurfaceType": "topo_data",
-            "topSurfaceName": "input/cookbook/test.topo",
-            "topNx": "32",
-            "topNz": "12",
-            "topMinX": "minX",
-            "topMaxX": "maxX",
-            "topMinZ": "minZ",
-            "topMaxZ": "maxZ",
-            
-            "bottomEquation": "x<1 ? -0.1*x : -0.1"
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "front",
-                "variables": [
-                    {
-                        "name": "vz",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "back",
-                "variables": [
-                    {
-                        "name": "vz",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "3",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/file.json
--- a/json_input/cookbook/file.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "type": "func",
-                        "value": "File1"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0",
-    "File1_Name": "input/cookbook/velocities",
-    "File1_Dim": "0",
-    "File1_N": "102"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/fixed_bottom.json
--- a/json_input/cookbook/fixed_bottom.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True",
-                "staticLeft" : "True",
-                "staticLeftTop" : "True",
-                "staticBottom" : "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "surfaceAdaptor":
-        {
-            "Type": "SurfaceAdaptor",
-            "mesh": "v-mesh",
-            "sourceGenerator": "v-mesh-generator",
-            "bottomEquation": "step(0.960468635615-x)*(-3 + sqrt(3.15*3.15 - x*x))"
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "r=hypot(x,y+3), step(3.35-r)*(y+3)"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "r=hypot(x,y+3), step(3.35-r)*(y+3)"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "r=hypot(x,y+3), -step(3.35-r)*x"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/inflow_outflow.json
--- a/json_input/cookbook/inflow_outflow.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True",
-                "staticLeft" : "True",
-                "staticBottom" : "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "step(y-0.1)*step(0.2-y)"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "step(x-0.9)*step(1.1-x)"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "-step(x-0.9)*step(1.1-x)"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/multi_material.json
--- a/json_input/cookbook/multi_material.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,138 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "sphereShape":
-        {
-            "Type": "EquationShape",
-            "equation": ".1^2 - ((x-1)^2 + (y-.15)^2)"
-        },
-        "nonsphereShape":
-        {
-            "Type": "Intersection",
-            "shapes":
-            [
-                "boxShape",
-                "!sphereShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "nonsphereShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "sphereViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "10.0"
-        },
-        "sphereViscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "sphereShape",
-            "density": "1.0",
-            "Rheology": [
-                "sphereViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/non_newtonian.json
--- a/json_input/cookbook/non_newtonian.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,224 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "T-mesh": "T-mesh",
-                "displacementField": "DisplacementField",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity",
-            "TemperatureField": "TemperatureField"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "sphereShape":
-        {
-            "Type": "EquationShape",
-            "equation": ".1^2 - ((x-1)^2 + (y-.15)^2)"
-        },
-        "nonsphereShape":
-        {
-            "Type": "Intersection",
-            "shapes":
-            [
-                "boxShape",
-                "!sphereShape"
-            ]
-        },
-        "nonNewtonian":
-        {
-            "Type": "NonNewtonian",
-            "StrainRateInvariantField": "StrainRateInvariantField",
-            "TemperatureField": "TemperatureField",
-            "n": "3.4",
-            "T_0": "1.0",
-            "A": "1.0",
-            "refStrainRate": "0.01"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "nonsphereShape",
-            "density": "1.0",
-            "alpha": "1.0",
-            "diffusivity": "1.0",
-            "heatingElements": [
-                {
-                    "Q": "1.0",
-                    "lambda": "1.0"
-                }
-            ],
-            "Rheology": [
-                "nonNewtonian",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "sphereViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "10.0"
-        },
-        "sphereViscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "sphereShape",
-            "density": "1.0",
-            "alpha": "10.0",
-            "diffusivity": "10.0",
-            "heatingElements": [
-                {
-                    "Q": "1000.0",
-                    "lambda": "10.0"
-                }
-            ],
-            "Rheology": [
-                "sphereViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.01"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureBCs": {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "2.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "TemperatureField",
-        "PressureField"
-    ],
-    "enable-thermal": true,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/normal_stress.json
--- a/json_input/cookbook/normal_stress.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,114 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True",
-                "staticBottom": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-        ,"stressBC":
-        {
-            "Type": "StressBC",
-            "ForceVector": "mom_force",
-            "wall": "bottom",
-            "normal_value": "0.35-y"
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/sinusoid.json
--- a/json_input/cookbook/sinusoid.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "backgroundShape":
-        {
-            "Type": "EquationShape",
-            "equation": "1"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "backgroundShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "surfaceAdaptor":
-        {
-            "Type": "SurfaceAdaptor",
-            "mesh":"v-mesh",
-            "sourceGenerator": "v-mesh-generator",
-            "topEquation": "0.1*sin(2*pi*x)"
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/split.json
--- a/json_input/cookbook/split.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,112 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "step(x-1)"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/template.json
--- a/json_input/cookbook/template.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/thermal.json
--- a/json_input/cookbook/thermal.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,219 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "T-mesh": "T-mesh",
-                "displacementField": "DisplacementField",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity",
-            "TemperatureField": "TemperatureField"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "sphereShape":
-        {
-            "Type": "EquationShape",
-            "equation": ".1^2 - ((x-1)^2 + (y-.15)^2)"
-        },
-        "nonsphereShape":
-        {
-            "Type": "Intersection",
-            "shapes":
-            [
-                "boxShape",
-                "!sphereShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "nonsphereShape",
-            "density": "1.0",
-            "alpha": "1.0",
-            "diffusivity": "1.0",
-            "heatingElements": [
-                {
-                    "Q": "1.0",
-                    "lambda": "1.0"
-                }
-            ],
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "sphereViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "10.0"
-        },
-        "sphereViscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "sphereShape",
-            "density": "1.0",
-            "alpha": "10.0",
-            "diffusivity": "10.0",
-            "heatingElements": [
-                {
-                    "Q": "1000.0",
-                    "lambda": "10.0"
-                }
-            ],
-            "Rheology": [
-                "sphereViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.01"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureBCs": {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "2.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "TemperatureField",
-        "PressureField"
-    ],
-    "enable-thermal": true,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/thermal_file.json
--- a/json_input/cookbook/thermal_file.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,225 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "T-mesh": "T-mesh",
-                "displacementField": "DisplacementField",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity",
-            "TemperatureField": "TemperatureField"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "sphereShape":
-        {
-            "Type": "EquationShape",
-            "equation": ".1^2 - ((x-1)^2 + (y-.15)^2)"
-        },
-        "nonsphereShape":
-        {
-            "Type": "Intersection",
-            "shapes":
-            [
-                "boxShape",
-                "!sphereShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "nonsphereShape",
-            "density": "1.0",
-            "alpha": "1.0",
-            "diffusivity": "1.0",
-            "heatingElements": [
-                {
-                    "Q": "1.0",
-                    "lambda": "1.0"
-                }
-            ],
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "sphereViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "10.0"
-        },
-        "sphereViscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "sphereShape",
-            "density": "1.0",
-            "alpha": "10.0",
-            "diffusivity": "10.0",
-            "heatingElements": [
-                {
-                    "Q": "1000.0",
-                    "lambda": "10.0"
-                }
-            ],
-            "Rheology": [
-                "sphereViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0.01"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureBCs": {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "2.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "temperature",
-                        "type": "func",
-                        "value": "File1"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "TemperatureField",
-        "PressureField"
-    ],
-    "enable-thermal": true,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "8",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0",
-    "File1_Name": "input/cookbook/temperatures",
-    "File1_Dim": "0",
-    "File1_N": "202",
-    "File1_Dim2": "1",
-    "File1_N2": "37"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/thermal_only.json
--- a/json_input/cookbook/thermal_only.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,190 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "T-mesh": "T-mesh",
-                "displacementField": "DisplacementField",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "sphereShape":
-        {
-            "Type": "EquationShape",
-            "equation": ".1^2 - ((x-1)^2 + (y-.15)^2)"
-        },
-        "nonsphereShape":
-        {
-            "Type": "Intersection",
-            "shapes":
-            [
-                "boxShape",
-                "!sphereShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "nonsphereShape",
-            "density": "1.0",
-            "alpha": "1.0",
-            "diffusivity": "1.0",
-            "heatingElements": [
-                {
-                    "Q": "1.0",
-                    "lambda": "1.0"
-                }
-            ],
-            "Rheology": [
-                "backgroundViscosity"
-            ]
-        },
-        "sphereViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "10.0"
-        },
-        "sphereViscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "sphereShape",
-            "density": "1.0",
-            "alpha": "10.0",
-            "diffusivity": "10.0",
-            "heatingElements": [
-                {
-                    "Q": "1000.0",
-                    "lambda": "10.0"
-                }
-            ],
-            "Rheology": [
-                "sphereViscosity"
-            ]
-        }
-    },
-    "velocityICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "vx",
-                        "value": "0.0"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "0.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureBCs": {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "top",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "temperature",
-                        "value": "2.0"
-                    }
-                ]
-            }
-        ]
-    },
-    "temperatureICs":
-    {
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "AllNodesVC",
-                "variables":[
-                    {
-                        "name": "temperature",
-                        "value": "1.0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "VelocityField",
-        "TemperatureField"
-    ],
-    "enable-thermal": true,
-    "enable-stokes": false,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/tracers.json
--- a/json_input/cookbook/tracers.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,150 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True",
-                "staticLeft" : "True",
-                "staticLeftTop" : "True",
-                "staticBottom" : "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "surfaceAdaptor":
-        {
-            "Type": "SurfaceAdaptor",
-            "mesh": "v-mesh",
-            "sourceGenerator": "v-mesh-generator",
-            "bottomEquation": "step(0.960468635615-x)*(-3 + sqrt(3.15*3.15 - x*x))"
-        },
-
-        "pLayout":
-        {
-            "Type": "ManualParticleLayout",
-            "totalInitialParticles": "1",
-            "manualParticlePositions": [
-                "asciidata",
-                ["x", "y"],
-                1.0, .1,
-                1.3, .1,
-                1.6, .1,
-                1.9, .1,
-                1.0, .2,
-                1.3, .2,
-                1.6, .2,
-                1.9, .2
-            ]
-        },
-        "swarmOutput":
-        {
-            "Type": "TracerOutput",
-            "Swarm": "passiveTracerSwarm",
-            "Fields" : [
-                "PressureField",
-                "StrainRateInvariantField"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "r=hypot(x,y+3), step(3.35-r)*(y+3)"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "r=hypot(x,y+3), step(3.35-r)*(y+3)"
-                    },
-                    {
-                        "name": "vy",
-                        "value": "r=hypot(x,y+3), -step(3.35-r)*x"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "enable-tracers": true,
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "100",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/viscous.json
--- a/json_input/cookbook/viscous.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "boxShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file
diff -r 8de894d93a65 -r 8630c321b820 json_input/cookbook/yielding.json
--- a/json_input/cookbook/yielding.json	Wed Nov 23 16:23:00 2011 -0800
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,165 +0,0 @@
-{
-    "EulerDeform":
-    {
-        "systems": [
-            {
-                "mesh": "v-mesh",
-                "p-mesh": "p-mesh",
-                "remesher": "velocityRemesher",
-                "velocityField": "VelocityField",
-                "wrapTop": "True"
-            }
-        ]
-    },
-    "components":
-    {
-        "buoyancyForceTerm":
-        {
-            "Type": "BuoyancyForceTerm",
-            "ForceVector": "mom_force",
-            "Swarm": "gaussSwarm",
-            "gravity": "gravity"
-        },
-        "boxShape":
-        {
-            "Type": "Box",
-            "startX": "minX",
-            "endX": "maxX",
-            "startY": "minY",
-            "endY": "maxY",
-            "startZ": "minZ",
-            "endZ": "maxZ"
-        },
-        "sphereShape":
-        {
-            "Type": "EquationShape",
-            "equation": ".1^2 - ((x-1)^2 + (y-.15)^2)"
-        },
-        "nonsphereShape":
-        {
-            "Type": "Intersection",
-            "shapes":
-            [
-                "boxShape",
-                "!sphereShape"
-            ]
-        },
-        "backgroundViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "1.0"
-        },
-        "strainWeakening":
-        {
-            "Type": "StrainWeakening",
-            "TimeIntegrator": "timeIntegrator",
-            "MaterialPointsSwarm": "materialSwarm",
-            "softeningStrain": "0.1",
-            "initialDamageFraction": "0.0",
-            "initialDamageWavenumber": "0.5",
-            "initialDamageFactor": "0.5",
-            "healingRate": "0.0"
-        },
-        "yielding":
-        {
-            "Type": "DruckerPrager",
-            "PressureField": "PressureField",
-            "VelocityGradientsField": "VelocityGradientsField",
-            "MaterialPointsSwarm": "materialSwarm",
-            "Context": "context",
-            "StrainWeakening": "strainWeakening",
-            "StrainRateField": "StrainRateField",
-            "cohesion": "1.0",
-            "cohesionAfterSoftening": "0.0001",
-            "frictionCoefficient": "0.0",
-            "frictionCoefficientAfterSoftening": "0.0",
-            "minimumViscosity": "1.0e-4"
-        },
-        "viscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "nonsphereShape",
-            "density": "1.0",
-            "Rheology": [
-                "backgroundViscosity",
-                 "yielding",
-                "storeViscosity",
-                "storeStress"
-            ]
-        },
-        "sphereViscosity":
-        {
-            "Type": "MaterialViscosity",
-            "eta0": "10.0"
-        },
-        "sphereViscous":
-        {
-            "Type": "RheologyMaterial",
-            "Shape": "sphereShape",
-            "density": "1.0",
-            "Rheology": [
-                "sphereViscosity",
-                "storeViscosity",
-                "storeStress"
-            ]
-        }
-    },
-    "velocityBCs" :{
-        "type": "CompositeVC",
-        "vcList": [
-            {
-                "type": "WallVC",
-                "wall": "left",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "right",
-                "variables": [
-                    {
-                        "name": "vx",
-                        "value": "1.0"
-                    }
-                ]
-            },
-            {
-                "type": "WallVC",
-                "wall": "bottom",
-                "variables": [
-                    {
-                        "name": "vy",
-                        "value": "0"
-                    }
-                ]
-            }
-        ]
-    },
-
-    "FieldVariablesToCheckpoint": [
-        "StrainRateInvariantField",
-        "VelocityField",
-        "PressureField"
-    ],
-    "timeIntegratorOrder": "1",
-    "maxTimeSteps": "10",
-    "outputPath": "./output",
-    "dim": "2",
-    "minX": "0",
-    "minY": "0",
-    "minZ": "0",
-    "maxX": "2",
-    "maxY": "0.35",
-    "maxZ": "0.3",
-    "nx": "16",
-    "ny": "4",
-    "nz": "4",
-    "particlesPerCell": "40",
-    "seed": "13",
-    "checkpointEvery": "1",
-    "gravity": "1.0"
-}
\ No newline at end of file



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